Motif seq in input seq and genes

Question

[kanwarjag]

I have identified a chip seq motif. How I can identify occurrences with statistical significance in the number seq that I used to identify such motif. I also want to identify occurrences of this motif in number of genes (names). What tool can be best used for this purpose?

Thanks

Answer 1

[Asaf]

MEME can be used to (re)identify the motif and evaluate its statistical significance. MAST can be then used to search for the motif in other regions of the genome. http://meme-suite.org/

Answer 2

[ivivek_ngs]

For sequences as Asaf highlighted MEME is good. For genes I would highlight 3 other. HOMER, PSCAN and iRegulon.